Example: Run a Slow-cooling Molecular Dynamics Simulation

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Example: Run a Slow-cooling Molecular Dynamics Simulation

The powerful X-PLOR shell language is able to produce a large number of possible cooling or heating schedules for simulated annealing (Kirkpatrick, Gelatt, and Vecchi, 1983). The example below uses a slow-cooling annealing schedule.

 set seed=432324368 end 

 vector do (vx=maxwell(4000.)) ( all )
 vector do (vy=maxwell(4000.)) ( all )
 vector do (vz=maxwell(4000.)) ( all )

 vector do (fbeta=100.) ( all )

 evaluate ($1=4000)
 while ($1 > 300.0) loop main     
          
    dynamics  verlet 
      timestep=0.0005            
      nstep=50
      iasvel=current 
      nprint=5  iprfrq=0
      tcoupling=true tbath=$1   
    end                                         
    evaluate ($1=$1-25)
 end loop main

Xplor-NIH 2025-03-21